title: Adult forebrain choroid plexus batch 1

city: Trondheim

first: Nathalie

last: Jurisch-Yaksi

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

data_processing:
QC quality control and adapter removal was done by Novogene (UK).
Mapping to reference genome (Danio rerio GRCz11 v.104) using STAR RNA-seq aligner (v. 2.7.2a)
Abundance quantified by RSEM (v. 1.3.3)
Counts from the 2 datasets were averaged in Zebrafish_count_table_all.csv
Assembly: GRCz11 v.104
Supplementary files format and content: RSEM files are tab-delimited text files for gene abundance for each samples in raw count, TPM and FPKM.
Supplementary files format and content: Zebrafish_count_table_all.csv contains the averaged counts from the 2 datasets

organism: Danio rerio

source_name: Forebrain choroid plexus

extract_protocol:
To extract total RNA from the fChP, adult zebrafish (Nacre and AB, 6 - 8-month-old) were euthanized by cold AFW and the brains were dissected out in cold aCSF. The fChPs were collected after removing the pineal gland. The dissected fChPs were kept temporarily in 1.5 mL tubes containing 20 μL RNAlater® (Thermo Fisher Scientific) on ice until RNA extraction steps started. Two batches of samples were prepared, and each batch had from 12 to 19 fChPs. To lyse the fChPs, TRIzol solution (500 μL, Thermo Fisher Scientific) was added and the tissues were homogenized through 27-gauge needles 15-18 times. More TRIzol (500 μL) was added into the tubes and the dissociated tissues were incubated for 5 min at RT. Chloroform (Sigma-Aldrich, 200 μL) was added to the samples and the tubes were inverted for several times to mix them. These were kept for 2 min at RT and centrifuged at 4°C for 15 min at 12,000 rpm. Then colorless supernatants including total RNAs were purified by two different methods using glycogen, or spin columns.  For the glycogen method, the RNA supernatant was transferred to a new tube and 0.5 μL glycogen solution (20 mg/mL, final glycogen mass: 10 μg) was added. Then, isopropanol (500 μL) was added to the sample, mixed by inverting and incubated on ice for 10 min. Then, the sample was centrifuged for 15 min at 12,000 rpm at 4°C. The supernatant was discarded, and the pellet was washed with 1 mL 70% ethanol (w/nuclease-free water) chilled at -20°C. The pellet was air-dried on ice for 2-5 min and dissolved in 70 μL nuclease-free water (Invitrogen). The sample was then treated with 10 μL DNase enzyme (QIAGEN) for 10 min at RT to remove DNA in the RNA samples. To isolate the RNAs, phenol-chloroform ethanol precipitation was performed. The DNase treated RNA sample was added to phenol-chloroform (pH8.0, company name, 100 μL) and mixed for 5-10 sec by inverting. The RNA was centrifuged for 8 min at 12,000 rpm at 4°C. The clear supernatant was transferred to a new tube, treated with chloroform (100 μL) and mixed for 5-10 sec by inverting. Following centrifugation at 12,000 rpm for 8 min at 4°C, the supernatant was precipitated with 10 μL 4M Ammonium Acetate buffer (100 μL) and 100% ethanol 330 μL for 30 min at -20°C and centrifuged at 12,000 rpm for 30 min at 4°C. The pellet was washed with 70% EtOH (w/nuclease-free water, 500 μL) and air dried on ice for 2-5 min. The pellet of RNAs was dissolved in 20 μL nuclease-free water (Thermo Fisher Scientific).  For the spin column method, the RNA supernatant was mixed to identical amount of isopropanol, loaded on RNA grade spin columns (QIAGEN, RNeasy Mini kit) and centrifuged for 30 sec at 8,000 rpm. The spin columns were washed with 700 μL Buffer RW1 and 350 μL Buffer RW1 followed by DNaseI enzyme treatment in Buffer RDD for 10 min (10μL DNaseI in 70 μL Buffer RDD per column) at RT. After treatment, the column was washed with 350 μL Buffer RW1 and 500μL Buffer RPE. To elute the RNAs from the columns, 20 μL nuclease-free water was added and incubated for 2 min. The RNAs were centrifuged for 1 min at 8000 rpm and collected in tubes. The concentrations of four eluted RNAs were quantified using Nanodrop (Thermo Fisher Scientific) and stored at -80°C before RNA sequencing. The quality of RNA samples was analysed by bioanalyzer at Novogene.
Due to low amount of quantity in the RNA samples, the RNAs were pre-amplified using by the SMARTer kit and RNA sequencing (paired-end 150 bp, with 12 Gb output) was performed on an Illumina NovaSeq 6000 (Illumina) at Novogene (UK).

value: Forebrain choroid plexus

tag: tissue type

value: Whole tissue

value: AB and nacre (mitfa-/-)

value: no treatment


title: Adult forebrain choroid plexus batch 2

status: Public on May 06 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment


title: Egr1 KO_PBS_1

city: Rehovot

first: Lingling

last: Zhang

address: Yavne Street 68, 68

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ragner software v7
Assembly: mm10
Supplementary files format and content: tar archive of tab-separated values files and matrix files from cellranger

organism: Mus musculus

source_name: heart

extract_protocol:
Single-cell preparation for single-cell RNA sequencing 1. Cardiac cells were isolated from mouse hearts 4 days after myocardial infarction using a neonatal heart dissociation kit Primary materials needed: Enzyme mixtures (Miltenyi Biotec, Cat# 130-098-373), surgery tools, butterfly (KRUUSE Butterfly, Cat# 121716), GentleMACS dissociator (Miltenyi Biotec, Cat# 130-093-235), ice-cold PBS, 10cm dish, 6-well plate, GentleMACS C-tube (Miltenyi Biotec, Cat# 130-093-237), 10cm injector, 70 μm strainer, 50ml tube, wide-bore tips. 1). Euthanize mice using CO2. 2). Perfuse the heart with 20 mL of ice-cold PBS. 3). Identify and cut the infarcted area, mainly the left ventricle. 4). Wash the tissue twice in ice-cold PBS, ensuring complete blood removal with tweezers. 5). Transfer the tissue to a 6-well plate with 2 ml of enzyme mixture. Chop the tissue into fine pieces using scissors and transfer each piece to a separate C-tube. Run the dissociator program once (gently shake if some tissue is stuck in the middle). 6). Follow the GentleMACS incubation protocol (15 min each, 3-4 times). 7). After incubation, spin down for a few seconds to let all the mixture settle at the C-tube bottom. Add 5 mL of medium to each C-tube and centrifuge at 1400rpm for 5 minutes at 4°C. 8). Remove the supernatant completely and suspend the pellet in 3.1 ml of ice-cold PBS for each C-tube, using 1 ml wide-bore tips. 9). Run the suspension through a 70 μm strainer, with a 15ml tube as a container. 2. Debris removal Primary materials needed: ice-cold PBS, Debris removal solution (Miltenyi Biotec, Cat# 130-109-398) 1). Add 900 μl of Debris Removal solution to each C tube. 2). Mix well by gently moving the pipette 10 times up and down using wide-bore tips. 3). Overlay very gently with 4 ml of ice-cold PBS. (Note: Tilt the tube and pipette very slowly to ensure the newly added PBS is not mixed with the cell suspension.) 4). Centrifuge at 1000g for 10 minutes at 4°C with full acceleration and full brake. Three phases will be formed. 5). Aspirate the two top phases thoroughly and gently using a vacuum and a 1 ml pipette. 6). Fill up with cold PBS to the final 15 ml. 7). Gently invert the tube three times. Do not vortex. 8). Centrifuge at 1000g for 10 minutes at 4°C. 9). Aspirate the supernatant completely. 3. Red Blood Cell Lysis Primary materials needed: MACS buffer (0.5% BSA, 2mM EDTA in PBS, pH 7.2) at room temperature (RT), RBC lysis buffer (Miltenyi Biotec, Cat# 130-094-183) at RT. 1). Resuspend the cell pellet in 1 ml MACS buffer at RT using wide-bore tips. 2). Add 10 mL of RBC lysis buffer at RT. Gently pipette up and down 10 times. 3). Incubate at room temperature for 2 minutes. 4). Centrifuge at 600g for 5 minutes at 4°C. Pipette off the supernatant completely. 4. Magnetic Labeling Primary materials needed: ice-cold MACS buffer, CD31 microbeads (Miltenyi Biotec, Cat# 130-097-418), CD45 microbeads (Miltenyi Biotec, Cat# 130-052-301), wide-bore tips (200um, 1ml), Maintain room temperature at 20 degrees Celsius (lower air conditioner). 1). Take one aliquot for calibration by FACS to determine the percentage of all cell types. 2). Mix microbeads before use. Incubate cell pellets with microbeads: 10ul CD45 + 10ul CD31 microbeads + 70ul MACS buffer. 3). Mix well and incubate microbeads for 15 minutes at 4-8 degrees (refrigerator, not on ice). Gently mix once every 5 minutes. Note: Working on ice may require increased incubation times. Higher temperatures or longer incubation times lead to non-specific cell labeling. 4). Add 1 mL of cold MACS buffer and centrifuge at 300g for 5 minutes at 4°C. 5). Remove the supernatant. Resuspend in 500 uL cold MACS buffer (Up to 108 total cells). Note: Work quickly, maintain cell coldness, and use pre-cooled solutions to prevent antibody capping on the cell surface and non-specific cell labeling. The volumes provided for magnetic labeling are for up to 107 total cells. For fewer than 107 cells, use the same volumes as indicated. Scale up all reagents and total volumes for higher cell numbers. 5. Magnetic Separation - This section is conducted in a cold room (4°C). Primary materials needed: MS column, OctoMACS separator (Miltenyi Biotec, Cat# 130-042-109), MACS buffer, Maintain a lower AC temperature (20°C). 1). Prepare the MS Column by rinsing with buffer: apply 500 μL of MACS buffer on top of the column and allow the buffer to run through. MS Columns are "flow stop," and should not run dry. (Filling with 500 μL takes ~1.5 minutes.) 2). Discard the effluent and change the collection tube. The MS Column is now ready for magnetic separation. 3). Apply the cell suspension onto the prepared MS Column. Collect the flow-through containing unlabeled cells. 4). Wash the MS column with 3X 500 μl of MACS buffer. Collect unlabeled cells that pass through and combine with the flow-through from the last step. (1st: ~1.5 min; 2nd: ~2 min; 3rd: ~3 min) Note: Perform washing steps by adding buffer aliquots as soon as the column reservoir is empty. 5). Remove the MS Column from the separator and place it on a new collection tube. 6). Pipette 1 mL of buffer onto the MS Column. Immediately flush out the fraction with the magnetically labeled cells by firmly applying the plunger supplied with the column. 7). Centrifuge the collected flow-through depletion cells (mainly cardiac fibroblasts)  and beads enriched cells (mostly immune cells) at 300g for 5 minutes at 4°C. 8). Resuspend the cells in 50-500 μl (adjusting based on the cell pellet size) ) of Cell Resuspension Buffer containing 0.04% BSA in PBS, pH 7.2. Count the cells and adjust the concentration to approximately 1X10⁶ cells/mL. 9). Combine 45 μl of depletion cells (~1X10⁶ cells/mL) with 15 μl of enriched cells (~1X10⁶ cells/mL) in one Eppendorf tube. Bring the samples for processing immediately. Note: Use the column immediately after filling to prevent the formation of air bubbles caused by warming up. Do not store columns after filling. The time required to fill the column with buffer depends on storage conditions, temperature, and humidity. Therefore, the filling time may vary from a few seconds to several minutes. This filling time does not influence the quality of the separation.
Library preparation and sequencing of scRNA-seq scRNA-seq was performed using the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3, 16 rxns (10x Genomics, PN-1000075) according to the manufacturer’s instructions and targeting a recovery of 6,000 cells per dataset. Each dataset was obtained with a sample size of three mouse biological replicates. The libraries were constructed as instructed in the manufacturer’s protocol. Sequencing was done on a Nova-Seq6000 using SP, 100 cycles kit mode allocating 800M reads in total (Illumina).The average read depth across the samples was 23,211 per cell.

value: heart

value: PBS


title: HDF cells, basal media treated, rep 2

city: Marietta

first: Isioma

last: Enwerem-Lackland

state: GA

address: 1775 W Oak Commons Ct

department: Research and Development

country: USA

institute: Mimedx

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house (Novogene) perl scripts
Paired-end reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis  was performed using the DESeq2 R package (1.20.0)
Assembly: hg38
Supplementary files format and content: excel file includes FPKM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: HDF

growth_protocol: Adult human dermal fibroblast cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humdified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA extraction was done at Novogene  using TRIzol following manufacturer's protocols
mRNA library preparation was done at Novogene

treatment_protocol: To initiate experiments under MMC conditions, human dermal fibroblast (HDF) cells were seeded in 100mm dishes at 10,000 cells/cm2 for each experiment. After 4 hours, cells were washed with basal DMEM, and starved overnight in DMEM containing 0.4% FBS, 1% penicillin streptomycin, and 1% sodium pyruvate followed by treatment of HDFs for six days. Culture media and treatments were replaced on day 3.  All treatments were carried out in DMEM containing 0.4% FBS, 1% penicillin streptomycin, 1% sodium pyruvate, 1 mM of L-ascorbic acid 2-phospate (Sigma-Aldrich, St. Louis, MO), and a mixture of 37.5 mg/mL Ficoll 70 kDa (Sigma-Aldrich, St. Louis, MO) and 25 mg/ml Ficoll 400 kDa (Sigma-Aldrich, St. Louis, MO). The following control groups were included for each experiment: Basal media and 10 ng/mL TGFβ1 (R&D Systems, Minneapolis, MN). Treatments were carried out with DHACM (20 mg/mL, 10 mg/mL, and 1 mg/mL) in the presence of 10 ng/mL TGFβ1. Extracts were prepared as described in Moreno et al, 2021.

tag: cell line

value: HDF

tag: cell type

value: Human dermal fibroblasts

value: WT

value: macromolecular crowding model + basal media


title: S1-seq_wt_timecourse_15dpp_rep3

city: New York

first: Soonjoung

last: Kim

email: kims16@mskcc.org, soonjk@yuhs.ac

state: New York

address: 430 East 67th Street

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer C

library_source: genomic

data_processing:
After Qubit quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. We obtained paired-end reads of 50 bp. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes. Base calls were perfomed using bcl2fastq software v.2.20 or bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500, NextSeq 2000, or HiSeq 4000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>. Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000.  (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).
Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.
Reads for S1, Exo7/T, or ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Maps were analyzed using R version 4.0.3 <http://www.r-project.org>.
Assembly: mm10
Supplementary files format and content: BigWig files contain read counts at positions of resection endpoints. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.

molecule: genomic DNA

source_name: testis

extract_protocol:
Testis cells from mice at indicated age were obtained as described previously (ref. 1). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing, and DNA was liberated by treatment with SDS and proteinase K as described previously (ref. 1).  (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020).
In-plug overhang removal with S1 endonuclease for S1-seq, exonuclease VII and exonuclease T for Exo7/T-seq, or exonuclease T for ExoT-seq, and adaptor ligation were performed as described previously (ref. 1, 2, 3) with minor modifications. In brief for S1-seq, plugs were washed in 0.5 ml of modified S1 buffer (50 mM sodium acetate, 280 mM NaCl, 4.5 mM ZnSO4, pH 4.7) for 30 min four times, treated with 9 units of S1 nulcease in 500 µl of modified S1 buffer at 37°C for 20 min and washed once with 1ml TE. For Exo7/T-seq, plugs were washed in 1 ml of exonuclease VII buffer for 15 min twice, treated with 50 units of exonuclease VII in 100 µl of exonuclease VII buffer at 37°C for 60 min and washed once with 1ml TE and followed by exonulcease T treamtment. For ExoT-seq, plugs were washed in 1 ml of NEBuffer 4 for 15 min 3 times, treated with 75 units of exonuclease T in 100 µl of NEBuffer 4 at 24°C for 90 min and washed 3 times with 8 ml of TE for 15 min. The nuclease treated ssDNA ends were further polished with T4 polymerase before the first adaptor ligation as previously described (ref. 1, 2, 3). After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously (ref. 1, 2, 3).  (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020).  (ref. 2) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017).  (ref. 3) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
S1-seq, Exo7/T-seq, ExoT-seq

value: testis

tag: strain

value: Spermatocytes

value: wild type

tag: age

value: 15 days post partum


title: S1-seq_wt_timecourse_14dpp_rep3

value: 14 days post partum


title: S1-seq_Rad50LF_14dpp_rep1


title: HDF cells, basal media treated, rep 3


title: WT_0min_Rep3

city: Columbia

first: Pallav

last: Singh

state: Missouri

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

data_processing:
Trimgalore 0.6.7 was used for removing Illumina adapters, ambiguous nucleotides (N’s), any sequence reads with total read length < 20 bp and the quality Phred score < 20
Hisat2 version 2.2.1 was used for alinging the sequences with the assembely
Cufflinks version 2.2.1 was used for obtaining the FPKM values as well as cuffdiff method within the package was used for finding out the differentially expressed genes
Assembly: TAIR10
Supplementary files format and content: annotated output with FPKM values in csv file format

organism: Arabidopsis thaliana

source_name: leaves

extract_protocol:
RNA was extracted using Plant RNeasy kit (Qiagen)
RNA libraries were prepared using standard Illumina protocols

value: leaves

tag: time

value: 0 min


title: S1-seq_wt_timecourse_13dpp_rep3

value: 13 days post partum


title: 2 Lifetime, rep 2, 1350 days

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

description:
WGBS
2-1748674

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the mm10 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: mm10
Supplementary files format and content: txt files with columns of chr, loc, cov, meth

source_name: blood

extract_protocol:
DNA was extracted from the sorted cells and then bisulfite treated using an EZ DNA Methylation-Direct kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina NovaSeq 6000 systems

value: blood

value: CD8 T cells

value: multi-lifetime iteratively stimulation


title: HDF cells, basal media treated, rep 1


title: Chip2A1

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

institute: Pacific Northwest National Laboratory

data_processing:
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the mouse genome using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Assembly: human genome GRCh38
Supplementary files format and content: .txt files represent number of raw read counts mapping to each gene

source_name: Human pancreatic islet cell

growth_protocol: Human pancreatic islets from two human donors (Prodo Laboratories) were acquired and cultured for 24 hr in pancreatic islet media (PIMS, Prodo Laboratories).

extract_protocol:
RNA was acquired through nanoSPLITS. RNA quality and quantity were analysed with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA‐Seq, The TruSeq stranded mRNA (cat#20020594) was used to generate cDNA library for illumina NextSeq550 platform according to the manufacture protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).

treatment_protocol: Single cells were dissociated with TrypLE for ~15-30 minutes, washed with PBS, stained with Calcein-AM/propidium iodide, and sorted onto nanoSPLITS chips using a cellenONE cell sorter.

value: Human pancreatic islet cell

value: primary cells from 2 human donors

tag: medium

tag: time point

value: 24 hour culture


title: Egr1 KO_Agrin

description: 10x Genomics

value: heart

value: Agrin


title: Egr1 WT_PBS_2

description: 10x Genomics

value: WT

value: PBS


title: S1-seq_wt_timecourse_12dpp_rep3

value: testis

value: Spermatocytes

value: 12 days post partum


title: e16_wildtp_rbiggxxx_bc774

city: Santa Cruz

first: Bin

last: Chen

state: CA

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

data_processing:
Paired end reads were trimmed to 25x25bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements plus the E.coli genome
Paired end reads that mapped to repeat elements or E.coli  were discarded. The remaining reads were mapped to the mm10 genome using Bowtie2 .
The set of Bowtie2 paired-end mappings was filtered, retaining only mappings having  genomic length less than or equal to 120bp.
The bam files of mappings were converted to coverage tracks across the genome with the bedtools programs, using options so that the end-to-end coverage of each paired-end read is used.
The coverage tracks were compressed into bigWig format.
Assembly: mm10
Supplementary files format and content: bigWig coverage tracks of the end-to-end mappings of the paired-end reads
Library strategy: CUT&Tag

source_name: cerebral cortex

extract_protocol:
E16 wt, hGFAP-Cre; Smofl/fl (smo cko) cortices (n=3 each group) were dissected, and cells were isolated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. For CUT&RUN, H3K27ac, H3K4me3, H3K27me3, and IgG antibodies were used. 10,000 cells were used for each experiment.
For CUT&RUN, DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7645-S).

value: cerebral cortex

tag: developmental stage

tag: antibody

value: rbiggxxx

value: wildtp

value: Cut&Run


title: Egr1 WT_PBS_1

description: 10x Genomics


title: e16_wildtp_rbiggxxx_bc776


title: AML191_H3K4me1_input_Ctrl

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description: genomic input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: broadPeak

source_name: lymphocyte

growth_protocol: Human EVI1 expressing AML191 cells were cultured in 20% FBS containing RPMI-1640 media + 10 ng/mL GMCSF.

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments. For Arima HiChIP, the manufacturer's protocol was followed for sample processing and DNA extraction for library generation.
Libraries were constructed following standard Illumina protocols for paired end indexing for ChIP-Seq. DNA fragments were PCR amplified for 12 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp. For Hi-ChIP, the Arima Genomics Hi-ChIP protocol was followed for indexing, library construction and amplification.

treatment_protocol: For ChIP-Seq analysis, 1 x 10^7 Human AML 191 cells were treated for 16 hours with DMSO, or 100 nM of BC2059 for 16 hours. Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 2.5 M Glycine for 5 minutes. Cells were washed with 1X PBS, harvested by centrifugation at 2000 rpm for 5 minutes and snap frozen with liquid nitrogen. Ultra-sonication was used to shear the chromatin for chromatin immunoprecipitation analyses. For Arima HiChIP, 20 x 10^6 cells were crosslinked with 2% formaldehyde for 10 minutes, then quenched with Stop Solution (Arima Genomics). 12 micrograms of chromatin were utilized for the H3K27Ac HiChIP assay following the manufacturer's protocol.

value: lymphocyte

value: Acute myeloid leukemia

value: Control


title: e16_wildtp_rbh3k4m3_bc773


title: AML191_H3K4me1_Ctrl

description: ChIP-Seq

value: H3K4Me1 Active Motif RRID:AB_2793284


title: Egr1 WT_Agrin

description: 10x Genomics


title: S1-seq_Rad50S_16dpp_tech_rep

value: 16 days post partum


title: e16_wildtp_rbiggxxx_bc775


title: Egr1_WT_Agrin_2

description: 10x Genomics


title: AML191_H3K4me1_BC

description: ChIP-Seq


title: S1-seq_Rad50S_16dpp


title: Egr1_WT_Agrin_1

description: 10x Genomics


title: e16_wildtp_rbh3k4m3_bc772


title: e16_wildtp_rbh3k4m3_bc771


title: AML191_BC2059_input

description: genomic input


title: S1-seq_Exo1DA_16dpp_rep1


title: Egr1_KO_PBS

description: 10x Genomics


title: AML191_Control_input

description: genomic input


title: e16_wildtp_rbh3k27a_bc770


title: S1-seq_Nbs1dBhet_14dpp_rep1

value: Nbs1{delta}B het

value: 14 days post partum


title: S1-seq_Nbs1dB_Exo1DA_16dpp_rep1

value: Nbs1{delta}B Exo1DA


title: e16_wildtp_rbh3k27a_bc769


title: Egr1_KO_Agrin_2

description: 10x Genomics

value: heart

value: Agrin


title: AML191_BC2059_H3K27Ac_Hi-ChIP 2

description: HiChIP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: broadPeak
Library strategy: HiChIP

value: H3K27Ac Active Motif RRID:AB_2793305


title: S1-seq_Nbs1dB_14dpp_rep2

value: testis

value: Spermatocytes


title: Egr1_WT_PBS

description: 10x Genomics

value: WT

value: PBS


title: AML191_H3K4me1_input_BC

description: genomic input


title: e16_wildtp_rbh3k27a_bc768

value: cerebral cortex

value: wildtp


title: S1-seq_Nbs1dB_14dpp_rep1


title: AML191_BC2059_H3K27Ac_Hi-ChIP 1

description: HiChIP

value: lymphocyte


title: Egr1_KO_Agrin_1

description: 10x Genomics


title: AML191_Ctrl_H3K27Ac_Hi_ChIP 2

description: HiChIP

value: Acute myeloid leukemia

value: Control, 16 hours


title: AML191_Ctrl_H3K27Ac_Hi_ChIP 1

description: HiChIP


title: E155_KO

city: Shanghai

first: Songyuan

last: Luo

state: --None--

address: 639 Zhi-Zao-Ju Road

country: China

institute: Shanghai Ninth People’s Hospital

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads to trim poly-A tail and adapter sequences. Cell barcodes and UMI were extracted. After that, we used STAR to map reads to the reference genome GRCm38 (ensemble version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Lower incisors

extract_protocol:
The lower incisor germs were carefully separated under a stereomicroscope using micro forceps and transferred into the pre-cooled PBS solution. Lower incisor germ cells from Six1 knockout mice at E15.5 and wild-type incisor germ cells at E14.5, E15.5, and E16.5 were obtained for scRNA-seq. Tissues were dissociated using 0.25% trypsin-EDTA at 37°C for 10 minutes, and the digested cells were passed through a 40 μm sterile filter to obtain the filtrate. The dissociated cells were resuspended in 0.2 ml of 1×DPBS and stained with trypan blue for cell viability counting.
The scRNA-seq library was constructed using the micro-well-based GEXSCOPE® Single Cell RNA Library Kit. The cell suspension was first diluted to 1.5×105-3.5×105 cells/ml with pre-chilled PBS for microwell chip experiments. Barcoding beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the barcoding beads to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. Sequencing was performed on the Illumina NovaSeq 6000 sequencing platform, generating paired-end reads with a length of 150bp.

value: Lower incisors


title: S1-seq_Mre11ATLD_14dpp_rep2


title: S1-seq_Mre11ATLD_14dpp_rep1


title: E165_WT

value: Wild type


title: e16_wildtp_rbh3k27m_bc765

value: Cut&Run


title: E155_WT


title: e16_smocko_rbiggxxx_bc748

value: rbiggxxx

value: smocko


title: AML191_Control_H3K27Ac

description: ChIP-Seq

value: Control


title: e16_wildtp_rbh3k27m_bc747


title: AML191_100BC_2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

growth_protocol: Cultured and patient-derived AML cells were cultured in 20% FBS containing RPMI media (AML191) supplemented with 10 ng/mL GM-CSF.

extract_protocol:
Bulk ATAC-Seq analysis was performed following the protocol of Buenrostro et al 2015. Tn5 transposase-tagmented genomic DNA was utilized to make libraries for next generation sequencing.
Bulk ATAC Sequencing Libraries were constructed following standard Illumina protocols for paired-end sample indexing with I7 and I5 sequencing indices. Indexed libraries were amplified for 10-12 cycles of PCR.

treatment_protocol: AML cells were treated with 100 nM of BC2059 for 16 hours at 37°C and cryopreserved in freezing buffer composed of 90% FBS+ 10% DMSO until the time of nuclei isolation and Tn5 tagmentation.


title: e16_wildtp_rbh3k27m_bc746


title: Six1_rep2

data_processing:
*library strategy
Raw data were trimmed from 3' end until the final base had a quality score > 30, using Trimgalore-0.4.5, discarding reads left with < 20 bp
Raw data were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS2 v2.2.7 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
We digested E15.5 Six1+/+ and Six1-/- mouse incisor dental germ cells with 0.25% trypsin, and 50 000 cells per sample were used in three biological replicates for H3K27ac CUT&Tag assay. We digested E12.5 wide-type  mouse incisor dental germ cells with 0.25% trypsin, and 50 000 cells per sample were used in two biological replicates for SIX1 CUT&Tag assay
Cleavage under targets and tagmentation (CUT and Tag) libraries were prepared by In-Situ ChIP Library Prep Kit (TD903, Vazyme, China).


title: E7T-seq_Mre11cHN_11wo

value: 11 weeks old


title: E145_WT


title: E7T-seq_Mre11cHN_9wo

value: 9 weeks old


title: e16_wildtp_rbh3k27m_bc767


title: AML191_BC2059_H3K27Ac

description: ChIP-Seq

value: H3K27Ac Active Motif RRID:AB_2793305


title: AML191_100BC_1


title: E7T-seq_Mre11cHN_7wo

value: testis

value: Spermatocytes

value: 7 weeks old


title: E7T-seq_Mre11cKO_5wo_rep1

value: 5 weeks old


title: Six1_rep1


title: e16_wildtp_rbh3k27m_bc745

value: cerebral cortex

value: wildtp


title: Bone marrow derived macrophages 5 [RNA-seq]

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

data_processing:
The raw RNA-seq reads were first assessed for quality using FastQC. Quality trimming were performed using cutadapt to remove reads with adaptor contaminants and low-quality bases. Reads pairs with either end too short (<25bps) were discarded from further analysis. Next, trimmed and filtered reads were aligned to the mouse transcriptome mm10 using STAR.
Reads pairs with either end too short (<25bps) were discarded from further analysis. Next, trimmed and filtered reads were aligned to the mouse transcriptome mm10 using STAR.
Uniquely aligned reads were counted at gene level using featureCounts and then normalized using DESeq2 package taking into account of RNA composition bias.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: brain tumors

growth_protocol: MG(F4/80+CD11b+CD45loLY6Clo/-LY6G-CD49dlo/-) and BMDM (F4/80+CD11b+CD45+LY6Clo/-LY6G-CD49dhigh) were FACS-sorted from brain tumors

extract_protocol:
Total RNA was isolated from cells using the Quick-RNA microprep kit (Zymo Research).  Sequencing was done with an Illumina NextSeq500 on high output mode to generate ~4x108 1 x 75bp reads.
Libraries were prepared from the extracted RNA using the QuantSeq 3’mRNA-seq Library Prep Kit-FWD (Lexogen) and then subject to Illumina based sequencing using manufacturer’s recommendations (Illumina).

treatment_protocol: Brain tumors (GL261) established orthotopically in the mouse brain

value: brain tumors

value: WT

value: FACS-sorted from isogenic GL261 brain tumors established orthotopically in the mouse brain


title: AML191_control_2


title: e16_wildtp_rbh3k27m_bc766


title: AML191_control_1


title: Bone marrow derived macrophages 2 [RNA-seq]


title: E155_WT_H3K27ac_rep3

value: Lower incisors

value: H3K27AC (Abcam, ab4729)


title: E155_KO_H3K27ac_rep2


title: e16_wildtp_rbh3k4m3_bc741

value: Cut&Run


title: e16_smocko_rbh3k27m_bc743

value: smocko


title: Microglia 2 [RNA-seq]


title: OCI-AML20 100 nM BC2059 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

growth_protocol: Cultured and patient-derived AML cells were cultured in 20% FBS containing RPMI media (AML191, UCSD-AML1) supplemented with 10 ng/mL GM-CSF. OCI-AML20 cells were cultured with OP9 stromal cells in Alpha-MEM media and supplemented with 20% FBS and 10 ng/mL GM-CSF.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make cDNA libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified , pooled and sequenced.
Stranded mRNA-Seq

treatment_protocol: AML cells were treated with VTP50469, OTX015, or the combination for 16 hours at 37°C and harvested into RNA lysis buffer.


title: OCI-AML20 100 nM BC2059 2


title: Bone marrow derived macrophages 1 [RNA-seq]


title: UCSD-AML1 100 nM BC2059 1


title: e16_wildtp_rbh3k4m3_bc740


title: E155_WT_H3K27ac_rep2


title: OCI-AML20 Control 1

value: Control


title: Microglia 1 [RNA-seq]


title: e16_wildtp_rbh3k4m3_bc742


title: OCI-AML20 Control 2


title: e16_smocko_rbh3k4m3_bc739


title: E155_KO_H3K27ac_rep1


title: Bone marrow derived macrophages 3 [RNA-seq]


title: Vascular，rep3

city: Wuhan

first: Wangling

last: Hu

state: Hubei

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410

institute: Wuhan union hospital

data_processing:
Quality Control, FASTQC(version 0.11.8)
Cell Filtering, Scrublet(version 0.2.3)
Demultiplexing, Cell Ranger (version 2.2.0),cellranger count --id=sample_id --transcriptome=path/to/ref/genome --fastqs=data_path --sample=sample_name
Alignment and Quantification,STAR(version 2.5.1b),STAR --genomeDir=path/to/genome --readFilesIn=reads_R1.fastq reads_R2.fastq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix=prefix_
Clustering, Seurat（version 4.0.2）, seurat_object <- FindClusters(seurat_object)
Assembly: mm10
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx

source_name: Vascular

growth_protocol: Abdominal Aortic Aneurysms was induced by elastase exposure in mice at the age of 8 to 12 weeks.Mice were sacrificed 14 days after the surgery, and the spleen and abdominal aorta were harvested.

extract_protocol:
To obtain single cells from an aorta, the whole aortas were minced into small pieces and then digested in 1X Aorta Dissociation Enzyme Stock Solution at 37°C for 1 h. Cell suspensions were prepared by filtering them through a cell strainer. To obtain single cells from a spleen, the whole tissue was ground and cell suspensions were prepared by filtering them through the same cell strainer as mentioned before. Then, cell suspensions were added to the lymphocyte separation medium and mononuclear cells were obtained after density gradient centrifugation.
Cell capture and cDNA synthesis were performed using a single-cell 5' Library and Gel Bead Kit (10× Genomics, 1000006) and Chromium Single Cell A Chip Kit (10× Genomics, 120236). The cell suspension (300-600 living cells per microliter determined by CountStar) was loaded onto the Chromium single-cell controller (10× Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. Approximately 10,000 cells were added to each channel, and the target cells recovered were estimated to be approximately 6,000 cells. Captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs.

value: Vascular

value: CD4+ T cells

value: PPE


title: Bone marrow derived macrophages 4 [RNA-seq]


title: e16_wildtp_rbh3k27a_bc737


title: Vascular，rep2

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410


title: UCSD-AML1 Control 2


title: E155_KO_H3K27ac_rep3


title: e16_smocko_rbh3k4m3_bc738


title: e16_smocko_rbh3k27m_bc744


title: E155_WT_H3K27ac_rep1


title: Microglia 3 [RNA-seq]


title: UCSD-AML1 100 nM BC2059 2


title: AML191 200 nM BC2059 2


title: e16_wildtp_rbh3k27a_bc735


title: UCSD-AML1 Control 1


title: 06 WT 1000 myoblasts

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

description:
DESeq2_results_MuSC_vs_Myoblast_with_counts.csv
53_Myob

data_processing:
mRNA expression was quantified with Kallisto v0.46.1 (parameters: --single --fragment-length 200 --sd 20). The GENCODE v.28 basic gene annotations was used for transcriptome information.
Transcript-level abundance estimates were collapse to the gene level using the “tximport”.
Differentially expressed genes were identify using DESeq2. P values were adjusted for multiple testing using the Independent Hypothesis Weighting procedure.
Supplementary files format and content: Comma-delimited files with the gene names, gene descriptions, normalized counts, RPM and LFC estimates and p-value from DESeq2.

source_name: Skeletal muscle

extract_protocol:
RNA was extracted from cells using the SMART (Takara) lysis bufer
Following the manufacturers instructions, libraries were constructed using the SMART-Seq HT kit (Takara, cat. #624456) and illumina adapters were added with the Nextera XT kit (Illumina, cat. # FC-131-1024, FC-131-1001)

value: Skeletal muscle

value: Primary myoblasts


title: Spleen，rep2

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410

source_name: Spleen

value: Spleen


title: Spleen，rep3

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410


title: AML191 Control 2


title: e16_wildtp_rbh3k27a_bc736


title: Vascular，rep1

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410


title: 05 WT freshly isolated 1000 muscle stem cells

description:
DESeq2_results_MuSC_vs_Myoblast_with_counts.csv
52_MuSC

value: Muscle stem cell


title: 04 WT freshly isolated 1000 muscle stem cells

description:
DESeq2_results_MuSC_vs_Myoblast_with_counts.csv
18_MuSC


title: 03 Nedd4L WT 1000 muscle stem cells

description:
DESeq2_results_Nedd4L_WT_KO_LFC_with_counts_and_RPM.csv
32_WT


title: e16_smocko_rbh3k27a_bc733

value: cerebral cortex


title: Ascending aorta, AD-ABR1

city: Hefei

first: Hui

last: Jiang

state: AnHui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

data_processing:
Cell Ranger (http://support.10xgenomics.com/single-cell/software/overview/welcome) uses an aligner called STAR (https://github.com/alexdobin/STAR).
Seurat is a popular R package that can perform QC, analysis, and exploration of scRNA-seq data ,which was originally developed as a clustering tool for scRNA-seq data.
Used likelihood-ratio test to find differential expression for a single cluster, compared to all other cells. We identified differentially expressed genes as following criteria:1) p_value ≤ 0.01. 2) log2 FC ≥ 0.26. log2 FC means log2 fold-chage of the average expression between the two groups. 3) The percentage of cells where the gene is detected in specific cluster > 10%.
Selected the top 10 genes as the marker genes according to the result of differentially expression genes. Then the expression distribution of each marker gene was demonstrated by using heat map and bubble diagram
Assembly: Mus musculus GRCm38
Supplementary files format and content: CellRanger v6.0 (https://github.com/10XGenomics/cellranger) to have the plane single-celled data (fastq format) for preliminary analysis.
Supplementary files format and content: Seurat v4.0 (https://satijalab.org/) for further follow-up analysis of the single-cell expression matrix.

source_name: blood vessel

extract_protocol:
The Single Cell 3’ Protocol upgrades short read sequencers to deliver a scalable microfluidic platform for 3’ digital gene expression profiling of 500–10000 individual cells per sample. The 10x™ GemCode™ Technology samples a pool of ~750000 barcodes to separately index each cell’s transcriptome. It does so by partitioning thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Barcode. Libraries are generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: ascending aorta

value: aortic dissection and ABR


title: e16_smocko_rbh3k27a_bc734


title: 04 WT 1000 myoblasts

description:
DESeq2_results_MuSC_vs_Myoblast_with_counts.csv
18_Myob

value: WT


title: AML191 200 nM BC2059 1


title: Ascending aorta, AD2

value: aortic dissection


title: Ascending aorta, AD-ABR2


title: e16smo_cy_cntrl_yz060

description: e16smo_cy_k27ac_3samp_mm10.stringent.peaks.bed.trk.bb

data_processing:
Paired end reads were trimmed to 25x25bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements.
Paired end reads that mapped to repeat elements were discarded. The remaining reads were mapped to the mm10 genome combined with the sacCer3 genome using Bowtie2.
Reads mapping to the sacCer3 genome were discarded. The remaining set of Bowtie2 paired-end mappings was filtered, retaining only mappings having  genomic length less than or equal to 75bp.
The bam files of mappings were converted to coverage tracks across the genome using bedTools.
The coverage was merged over groups of 3 samples of the same genotype and antibody.
For each genotype, the coverage of an antibody was compared to the coverage of the control antibody using the SEACR program with the "norm" and "stringent" parameters.
The SEACR bed file of peaks was converted to a track in the bigBed format
Assembly: mm10
Supplementary files format and content: bigBed of SEACR peak loci
Library strategy: CUT&Tag

extract_protocol:
Rosa26SmoM2/+ (smo_cn), and hGFAP-Cre; Rosa26SmoM2/+ cortices (smo_cy) (n=3 each group) were dissected, and cells were isolated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. For CUT&RUN, H3K27ac, H3K4me3, H3K27me3, and IgG (cntrl) antibodies were used. 10,000 cells were used for each experiment.
For CUT&RUN, DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7645-S).

value: cntrl IgG

value: smoM2; hGFAP-cre


title: e16smo_cy_cntrl_yz084

value: Cut&Run


title: IIT_RDT_REP2_FUS-P525L_IP_S20

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, m6A-IP, Replicate2
peaks.exomepeaks2.bed

data_processing:
Trimmomatic (v0.39; Bolger et al., 2014) and Cutadapt (v3.2; Martin, 2011) were used to remove adapter sequences and poor quality bases; minimum read length after trimming was set to 35.
Reads aligning to rRNAs were filtered out; this first alignment was performed using Bowtie2 software (v2.4.2, https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
STAR software (v2.7.7a, Dolbin et al., 2013) was used to align reads to GRCh38 genome.
PCR duplicates were removed from all samples using MarkDuplicates command from Picard suite (v2.24.1; https://broadinstitute.github.io/picard/).
Multi-mapped and un-properly paired reads were filtered out using bamtools (v2.5.1; Barnett et al., 2009)
Peak calling was performed using exomePeak2 (v1.9.1) (https://github.com/ZW-xjtlu/exomePeak2)
Meta-gene peak coverage and motif enrichment analysis was performed with RNAmod(Liu & Gregory, 2019).
Reads coverage for the forward and reverse strand were generated using deepTools bamCoverage software (v3.5.1; https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html).
see Material and Methods
Assembly: GRCh38
Supplementary files format and content: peaks.exomepeaks2.bed

source_name: SK-N-BE

growth_protocol: SK-N-BE cells were cultured in RPMI (Sigma-Aldrich, Saint Louis, MO, USA) supplemented with 10% FBS (Sigma-Aldrich, #F2442), GlutaMAX supplement 1X (ThermoFisher Scientific, # 35050061), sodium-pyruvate 1mM (Thermo Fisher Scientific, #11360070) and Pen/Strep 1X (Sigma-Aldrich, #P4458).

extract_protocol:
Poly-A fragmented RNA was recovered through standard phenol-chloroform extraction and precipitation.
RNA libraries for RNA-seq were prepared using Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) following manufacturer's protocols.

treatment_protocol: 2x106 SK-N-BE cells FUSP525L were plated on a 6cm plate and transfected with 4ug of vectors expressing sh1 and 4 ug of sh2 (TRCN0000289812, TRCN0000289814). The day after cells were transferred to a 15cm plates. When required, 96hr after transfection FUS expression was induced with doxycycline for 24hr, stressed 1hr before harvesting, and harvested according to the protocol described by Khong et al. (2017). For the inducible expression of FUS-FLAG P525L, SK-N-BE cells were exposed to 50 ng/mL Doxycycline (Sigma-Aldrich, #D9891) for 24h before the sodium arsenite treatment (Sigma-Aldrich, #106277).  For acute oxidative stress treatment, SK-N-BE cells were exposed to 0.5 mM sodium arsenite for 1 hr.

value: SK-N-BE

value: Neuroblastoma

value: Doxycycline, Arsenite

tag: fraction

value: IP


title: e16smo_cy_cntrl_yz072


title: Ascending aorta, AD1


title: 02 Nedd4L WT 1000 muscle stem cells

description:
DESeq2_results_Nedd4L_WT_KO_LFC_with_counts_and_RPM.csv
08_WT


title: IIT_RDT_REP2_FUS-P525L_INPUT_S30

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, Input, Replicate2
peaks.exomepeaks2.bed

value: INPUT


title: 05 WT 1000 myoblasts

description:
DESeq2_results_MuSC_vs_Myoblast_with_counts.csv
52_Myob

value: Skeletal muscle


title: 06 WT freshly isolated 1000 muscle stem cells

description:
DESeq2_results_MuSC_vs_Myoblast_with_counts.csv
53_MuSC


title: Spleen，rep1

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410

value: CD4+ T cells

value: PPE


title: AML191 Control 1

value: Control


title: e16smo_cn_cntrl_yz090

description: e16smo_cn_k27ac_3samp_mm10.stringent.peaks.bed.trk.bb

value: cerebral cortex

value: smoM2; no cre


title: IIT_RDT_REP1_FUS-P525L_INPUT_S48

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, Input, Replicate1
peaks.exomepeaks2.bed


title: e16smo_cn_cntrl_yz078


title: IIT_RDT_REP1_FUS-P525L_IP_S23

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, m6A-IP, Replicate1
peaks.exomepeaks2.bed


title: 03 Nedd4L-cKO 1000 muscle stem cells

description:
DESeq2_results_Nedd4L_WT_KO_LFC_with_counts_and_RPM.csv
55_KO

value: Muscle stem cell


title: 01 Nedd4L WT 1000 muscle stem cells

description:
DESeq2_results_Nedd4L_WT_KO_LFC_with_counts_and_RPM.csv
04_WT

value: WT


title: e16smo_cn_cntrl_yz066


title: 01 Nedd4L-WT 5000 freshly isolated muscle stem cells

data_processing:
Adapters were removed from raw ATAC-seq reads using Trimmomatic (version 0.39, parameters: LEADING:10 TRAILING:10 MINLEN:50).
Paired reads were aligned to mm10 using BWA-MEM (version 0.7.17).
Samtools was used to index and filter (version 1.16.1, mapping quality > 30).
Duplicated reads were removed using Picard (version 2.26.3).
ATAC-seq peaks were called with MACS2 (version 2.2.7.1, parameters: --nomodel --shift -100 --extsize 200 –broad, --gsize mm).
Assembly: mm10
Supplementary files format and content: tab-delimited text files describing the Broad and gapped peak (*_peaks.broadPeak, *_peaks.gappedPeak, and *_peaks.xls).

extract_protocol:
Cells were sorted into ATAC-Seq Lysis buffer(10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin) and then washed in a wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). After, the cells were centrifuged at 800g and DNA tagementation could be performed using the transposition mixture (5 μl of Tagment DNA (TD) buffer, 3.2 μl PBS, 0.89 μl Tn5, 0.1% Tween-20, 0.01% Digitonin and 0.75 μl water) for 20 minutes at 37oC.
Sequencing ready libaries were prepared by incorporating Illumina adaptors with PCR and then purifying and size selecting the DNA using AMPure beads


title: DOXY+_ARS+_shMETTL3_FUS-WT_SGenr_REP1_S49

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT, Doxycycline, Arsenite treated, sh-METTL3, SG-enriched sample, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

data_processing:
Trimmomatic (v0.39; Bolger et al., 2014) and Cutadapt (v3.2; Martin, 2011) were used to remove adapter sequences and poor quality bases; minimum read length after trimming was set to 35.
Reads aligning to rRNAs were filtered out; this first alignment was performed using Bowtie2 software (v2.4.2, https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
STAR software (v2.7.7a, Dolbin et al., 2013) was used to align reads to GRCh38 genome.
PCR duplicates were removed from all samples using MarkDuplicates command from Picard suite (v2.24.1; https://broadinstitute.github.io/picard/).
Uniquely mapping fragments were counted for each annotated gene (ensembl release 99) using htseq-counts software (v0.13.5; Anders et al., 2015). See Material and Methods section for further explanation.
Assembly: GRCh38
Supplementary files format and content: counts_table.tsv contains fragment counts for each gene. Counts were performed using htseq-counts algorithm (v0.13.5; Anders et al., 2015).
Supplementary files format and content: gene_quantification_table.FPKM_withoutTMM.tsv contains FPKMs gene quantifications

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep (Zymo Research) kit according to the manufacturer’s specifications.
RNA libraries for RNA-seq were prepared using Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) following manufacturer's protocols.

treatment_protocol: 2x106 SK-N-BE cells FUSWT or FUSP525L were plated on a 6cm plate and transfected with 4ug of vectors expressing sh1 and 4ug of sh2 (TRCN0000289812, TRCN0000289814). The day after cells were transferred to a 15cm plates. When required, 96hr after transfection FUS expression was induced with doxycycline for 24hr, stressed 1hr before harvesting, and harvested according to the protocol described by Khong et al. (2017). For the inducible expression of FUS-FLAG WT or P525L, SK-N-BE cells were exposed to 50 ng/mL Doxycycline (Sigma-Aldrich, #D9891) for 24h before the sodium arsenite treatment (Sigma-Aldrich, #106277).  For acute oxidative stress treatment, SK-N-BE cells were exposed to 0.5 mM sodium arsenite for 1 hr.

value: Doxycycline,Arsenite, shMETTL3

value: SG-enriched


title: e16smo_cy_k4me3_yz085

description: e16smo_cy_k4me3_3samp_mm10.stringent.peaks.bed.trk.bb

value: smoM2; hGFAP-cre


title: 04 Nedd4L-cKO 5000 freshly isolated muscle stem cells


title: 03 Nedd4L-cKO 5000 freshly isolated muscle stem cells


title: 01 Nedd4L-cKO 1000 muscle stem cells

description:
DESeq2_results_Nedd4L_WT_KO_LFC_with_counts_and_RPM.csv
22_KO


title: e16smo_cy_k4me3_yz061

value: Cut&Run


title: DOXY+_ARS+_shMETTL3_FUS-WT_INP_REP2_S13

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT, Doxycycline, Arsenite treated, sh-METTL3, Input, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: SK-N-BE

value: Input


title: L cells, batch2, HTO

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

description:
batch2.barcodes.tsv.gz
batch2.features.tsv.gz
batch2.matrix.mtx.gz

library_source: other

data_processing:
base calling using Illumina Bcl2fastq
alignment against an intron-to-exon converted reference using 10X cellranger V6.0.0
downstream analysis including QC filtering and other statistical analysis using Seurat V4.1.0
Assembly: UCSC mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx).  Hashtag_feature_reference.csv (Hashtag Antibody Information).

molecule: protein

source_name: L cell

extract_protocol:
The intestine was dissected, flushed twice with ice-code PBS and cut open longitudinally with scissors. After rinsing again with PBS, the intestine was cut into 2 cm segments and incubated in the isolation buffer (PBS, 2 mM EDTA, 3% FBS, 1 mM DTT) with gentle rocking at 37C for 30 mins. Epithelial cells were harvested by filtering through 100 um cell strainers, followed by spinning down at 400 x g for 10 mins at 4°C. Cells were resuspended in FACS buffer (PBS, 2mM EDTA, 0.2% BSA) and L cells (GFP+) were sorted with a FACSAria Fusion Flow Cytometer (BD Biosciences).
RNA libraries were prepared with Chromium Single Cell 3' Reagent Kits (V2) according to the manufacturer's instruction

treatment_protocol: GcgCre:GFP mice were treated with the antibiotic cocktail and colonized with Desulfovibrio for 2 weeks.

value: L cell

value: antibiotic cocktail, followed by Desulfovibrio colonization

tag: library type

value: Antibody Capture

tag: hashtag for antibiotics

value: Hashtag 1

tag: hashtag for desulfovibrio colonization

value: Hashtag 2


title: L cells, batch1, HTO

description:
batch1.barcodes.tsv.gz
batch1.features.tsv.gz
batch1.matrix.mtx.gz


title: DOXY+_ARS+_shMETTL3_FUS-WT_INP_REP1_S26

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT, Doxycycline, Arsenite treated, sh-METTL3, Input, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: Neuroblastoma


title: 02 Nedd4L-cKO 5000 freshly isolated muscle stem cells

value: Skeletal muscle


title: e16smo_cy_k27m3_yz087

description: e16smo_cy_k27m3_3samp_mm10.stringent.peaks.bed.trk.bb

value: cerebral cortex


title: L cells, batch2, GEX

value: Gene Expression


title: DOXY+_ARS+_shMETTL3_FUS-P525L_SGenr_REP2_S62

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, sh-METTL3, SG-enriched sample, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv


title: 01 Nedd4L-cKO 5000 freshly isolated muscle stem cells

value: Muscle stem cell


title: e16smo_cy_k27m3_yz075


title: 03 Nedd4L-WT 5000 freshly isolated muscle stem cells


title: 02 Nedd4L-WT 5000 freshly isolated muscle stem cells


title: DOXY+_ARS+_shMETTL3_FUS-WT_SGenr_REP2_S15

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT,  Doxycycline, Arsenite treated, sh-METTL3, SG-enriched sample, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv


title: 02 Nedd4L-cKO 1000 muscle stem cells

description:
DESeq2_results_Nedd4L_WT_KO_LFC_with_counts_and_RPM.csv
54_KO


title: L cells, batch1, GEX


title: DOXY+_ARS+_shMETTL3_FUS-P525L_SGenr_REP1_S44

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, sh-METTL3, SG-enriched sample, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv


title: GLUTag, GSH_rep3

data_processing:
HISAT2 (v 2.2.1) RNA-sequencing alignment software was used for  for mapping next-generation sequencing reads to mouse genome with following parameters: -3 30.
SAMtools (v 1.6) was used for filtering and sorting mapped reads with following parameters: samtools view -q 5; samtools sort -T -n.
FeatureCounts(v 2.0.1) was used for counting reads in features.
Data was normalized with R (v 4.1.2) and Limma-Voom (v 3.46.0) and log2-transformed
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for each gene in each sample. Matrix table with raw gene counts for each gene in each sample.

source_name: GLUTag

growth_protocol: Twelve-well cell culture plates were coated with 10 μg/mL poly-D-lysine overnight at 37°C. GLUTag cells were seeded at the density of 5 x 105 cells/well and cultured in DMEM containing 10% FBS and 1x penicillin-streptomycin solution for 48 hrs.

extract_protocol:
RNA were extracted by QIAGEN RNeasy Mini Kit (74116) following the manufacturers' instructions.
Stranded mRNA library were constructed by using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina ®(NR602) under manufacturers' protocol.

treatment_protocol: Cells were washed once with DPBS and incubated with 1mM NaHS or 0.33 mM GSH in DMEM for 2 hrs. Cells were harvested for RNA extraction and RNA-sequencing.

value: GLUTag

tag: batch

value: GSH


title: DOXY+_ARS+_shMETTL3_FUS-P525L_INP_REP2_S45

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline, Arsenite treated, sh-METTL3, Input, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: Doxycycline,Arsenite, shMETTL3


title: e16smo_cy_k27m3_yz063

tag: tissue

value: smoM2; hGFAP-cre


title: GLUTag, GSH_rep2


title: e16smo_cy_k4me3_yz073

tag: genotype

value: Cut&Run


title: e16smo_cy_k27ac_yz086

description: e16smo_cy_k27ac_3samp_mm10.stringent.peaks.bed.trk.bb

tag: treatment


title: DOXY+_ARS+_shMETTL3_FUS-P525L_INP_REP1_S43

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L, Doxycycline , Arsenite treated, sh-METTL3, Input, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

tag: cell line

value: SK-N-BE


title: kidney, TG, day7 [TG_270]

city: Lugano

first: Anna

last: Rinaldi

state: Ticino

address: Tesserete

department: Nephrology

country: Switzerland

institute: Ente Ospedaliero Cantonale

description: 10x Genomics

data_processing:
Sequencing data were processed by CellRanger (version 6.0.0) and reads were aligned to mouse pre-mRNA reference genome (mm10-2020-A) with STAR (v.2.5.1b)
The Cell Ranger cellranger count function output filtered gene–cell expression matrices, removing cell barcodes not represented in cells.
UMI count table utilizing both exonic and intronic reads was generated for downstream analysis.
Assembly: mouse pre-mRNA reference genome (mm10-2020-A)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Mice were perfused with ice-cold PBS and kidney halves collected for snRNA-seq analysis. Half kidney was cut into small pieces (>25) and transferred into a 2-ml Dounce homogenizer (Sigma, Cat#D8938) loaded with 1 ml of NEZ Lysis Buffer (Sigma, Cat#N3408) with RNase inhibitor (NEB, Cat#M0314) at final concentration of 0.4U/µl) on ice. Samples were then Dounce homogenized on ice with five strokes of the looser pestle every 2 min for 8 min (25 strokes in total). Samples were then slowly Dounce homogenized 25 times with the tighter pestle on ice. The  homogenized sample was filtered through a 40-μm Falcon Nylon Cell Strainer, then the filter was washed with 8 ml of 1% BSA PBS, and the nuclear suspension spun in a precooled (4 °C) centrifuge at 650g for 8 min. Supernatant was removed and the pellet resuspended in 1% BSA PBS (plus RNase inhibitor) and moved to a low-bind Eppendorf tube. Nuclear quality and number were assessed with trypan blue staining. Nuclei were sorted as DAPI positive on a BD Aria into 2% BSA solution with RNA inhibitor.
Barcoded single-cell gel beads in emulsion (GEMs) were created by 10x Genomics Chromium TM and then reverse transcribed to generate single-cell RNA-seq libraries using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s instructions

value: kidney

value: TG

value: FVB


title: GLUTag, GSH_rep1


title: kidney, TG, day7 [TG_271]

description: 10x Genomics


title: DOXY-_ARS+_shMETTL3_FUS-WT_SGenr_REP2_S59

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, SG-enriched sample, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

tag: cell type

value: Arsenite, shMETTL3

value: SG-enriched


title: e16smo_cy_k27ac_yz062


title: DOXY-_ARS+_shMETTL3_FUS-WT_SGenr_REP1_S29

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, SG-enriched sample, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv


title: kidney, TG saline control, day7 [TG_S_119]

description: 10x Genomics

tag: strain


title: e16smo_cy_k27ac_yz074


title: GLUTag, NaHS_rep2

value: NaHS


title: e16smo_cn_k4me3_yz091

description: e16smo_cn_k4me3_3samp_mm10.stringent.peaks.bed.trk.bb

value: smoM2; no cre


title: DOXY-_ARS+_shMETTL3_FUS-WT_INP_REP2_S21

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, Input, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: Neuroblastoma

value: Input


title: kidney, WT, day28 [WT_10995]

description: 10x Genomics

value: WT


title: GLUTag, NaHS_rep1


title: e16smo_cn_k4me3_yz079

value: cerebral cortex


title: DOXY-_ARS+_shMETTL3_FUS-WT_INP_REP1_S3

description:
SK-N-BE stable cell line with doxycycline inducible FUS-WT,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, Input, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv


title: kidney, TG, day28 [TG_11073]

description: 10x Genomics


title: GLUTag, Control_rep3

value: GLUTag

value: Control(DMEM)


title: e16smo_cn_k4me3_yz067


title: e16smo_cn_k27m3_yz093

description: e16smo_cn_k27m3_3samp_mm10.stringent.peaks.bed.trk.bb


title: GLUTag, Control_rep2


title: GLUTag, Control_rep1


title: DOXY-_ARS+_shMETTL3_FUS-P525L_SGenr_REP2_S42

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, SG-enriched sample, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv


title: kidney, TG, day28 [TG_10988]

description: 10x Genomics


title: e16smo_cn_k27m3_yz081


title: kidney, TG, day28 [TG11002]

description: 10x Genomics


title: Mouse19_TCRb_KO

data_processing:
16S data was trimmed by Cutadapt(v 4.1) and analyzed using QIIME2 (v2018.6). DADA2 procedure with default parameters was used for the pre-processing steps
The alpha and beta diversity analysis were calculated in R by using the phyloseq and microbiome package (http://microbiome.github.com/microbiome).
Differential abundance analysis was performed using Linear discriminant analysis effect size (LEfSe) with an LDA score threshold of > 3.8 and the Kruskal-Wallis test (α < 0.01), and the more stringent ANCOM were used to validate the results.
Assembly: SILVA 128
Supplementary files format and content: rds file containing colony OTU
Library strategy: 16s rRNA-seq

organism: feces metagenome

extract_protocol:
Microbial genomic DNA were extracted with a QIAamp DNA Stool Mini Kit (Qiagen, 51504) following the manufacturer’s instructions and eluted into 200 uL ddH2O. DNA was concentrated with a Quick-DNA Microprep Kit (Zymo, D3020).
PCR for V3 and V4 hypervariable regions using barcoded primers. Sequencing adaptor were added to purified PCR product under manufacturers' guide.
DNA library

treatment_protocol: Self-maintained as above or co-housed for 4 weeks.

value: Fecal pellets

value: TCRb-/-


title: kidney, TG, day7 [TG_269]

description: 10x Genomics


title: kidney, TG, day28 [TG11074]

description: 10x Genomics


title: GLUTag, NaHS_rep3


title: e16smo_cn_k27m3_yz069

value: Cut&Run


title: DOXY-_ARS+_shMETTL3_FUS-P525L_INP_REP2_S20

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, Input, Replicate2
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: SK-N-BE


title: Mouse18_WT


title: Sorted CD45- CD31- of CS3392

city: Singapore

first: Jing Quan

last: Lim

address: 30 Hospital Boulevard

department: CMR

country: Singapore

institute: National Cancer Centre Singapore

description: Sorted lymph nodal cells

data_processing:
The reads were demultiplexed and aligned against the GRCh38 reference genome using 10X Cell Ranger v6.0.1 (10X Genomics, CA, USA). The single-cell data were loaded into count matrices, and all 10 samples were merged using Seurat v4.1.
A total of 94,947 cells, which had less than 20% of transcripts mapping to mitochondrial genes and expressed at least 500 genes were retained for scaling, log-normalization of gene expression measurements, and principal component analysis with the top 2,000 genes selected by variance stabilizing transformation approach as implemented by Seurat, in addition to the 14 mitochondrial/rRNA genes (MT-ND1, MT-ND2, MT-CO1, MT-CO2, MT-ATP8, MT-ATP6, MT-CO3, MT-ND3, MT-ND4L, MT-ND4, MT-ND5, MT-ND6, MT-CYB, and RN7SL832P) that were removed from the dataset using our in-house annotated blacklist genes.
UMAP was used to visualize the distribution of cells in the projection of the significant principal components, and cell type annotation was accomplished with known markers from each cell type.
Up-regulated genes from each group were used for gene enrichment analysis with Gene Ontology (GO) Biological Process using enrichR.
To explore the effect of rituximab treatment, all six longitudinal PBMC samples from Twin-CS were merged and analyzed.
Assembly: GRCh38
Supplementary files format and content: all .h5 files: Each h5 contains the processed count matrixes, genes info and cell barcodes for each of our 12 scRNA-seq samples.

extract_protocol:
Single-cell RNA-seq (scRNAseq) libraries were prepared from tissue samples from Twin-CS (lymph node and bone marrow), as well as from peripheral blood mononuclear cells (PBMC) from the affected twins and unaffected sister. Tissues were dissociated into single cells using the Tumour Dissociation Kit, human (Miltenyi Biotec, Bergisch Gladbach, Germany) as per manufacturer’s protocol.
Each cell was captured and uniquely-barcoded using the 10X Chromium Next GEM Single Cell 5' Kit v2 (PN1000265) and 10X Chromium Controller according to manufacturer’s protocol (10X Genomics, CA, USA). Following Gel Beads-in-emulsion (GEMs) generation, cell lysis and dissolution of the Gel Bead within each reaction vesicle enabled reverse transcription of polyadenylated mRNA, producing cDNA tagged with both a universal cell barcode and unique molecular index (UMI). The reaction vesicles were then lysed for cDNA amplification followed by purification using Dynabeads MyOne SILANE magnetic beads. Quantification of cDNA was performed using Agilent Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies, CA, USA). The generated cDNA from each sample was used for 5’ gene expression (5'GEX) scRNA-seq library generation. Enzymatic fragmentation of the cDNA transcripts was carried out, followed by End-Repair and A-tailing, adaptor ligation and final library amplification PCR with unique sample indices for each sample. Final library quality was determined using the Agilent Bioanalyzer High Sensitivity DNA Kit.
scRNA-seq 10X 5' kit v2

tag: Sex

value: female

value: sorted cells


title: e16smo_cn_k27ac_yz080

description: e16smo_cn_k27ac_3samp_mm10.stringent.peaks.bed.trk.bb


title: kidney, WT, day28 [WT11076]

description: 10x Genomics

value: kidney

value: FVB


title: Sorted CD45- CD31+ of CS3392

description: Sorted lymph nodal cells


title: S106_wdah_RU-_gut_rep5

city: LONDON

first: MengJia

last: Li

state: Please Select

address: flat38 midhopse house, midhope street

country: United Kingdom

institute: University College London

data_processing:
Quality control with fastqc
Alignment with hisat2
Read counts with featureCounts
Differentially expression analysis with deseq2
Salmon to confirm Xbp1U samples
Assembly: Drosophila Melanogaster dm6 (r6.47)
Supplementary files format and content: Differentially expression results for each genotype/tissues

organism: Drosophila melanogaster

source_name: Gut

extract_protocol:
Trizol_cholofrom
pair-end

treatment_protocol: treat with RU486 +/- for 7 days

value: Gut

value: RU-


title: S106_wdah_RU-_gut_rep4


title: Mouse16_TCRb_KO_co_housed


title: e16smo_cn_k27ac_yz068

value: smoM2; no cre


title: e16smo_cn_k27ac_yz092


title: Lymph node of CS3392

description: Fresh lymph node tissue

source_name: Lymph Node

value: Lymph Node

value: fresh tissue


title: S106_wdah_RU-_gut_rep3


title: DOXY-_ARS+_shMETTL3_FUS-P525L_SGenr_REP1_S7

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, SG-enriched sample, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: Neuroblastoma

value: Arsenite, shMETTL3

value: SG-enriched


title: e16_shh_yz017

data_processing:
Paired end reads were trimmed to 40x40bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements.
Paired end reads that mapped to repeat elements were discarded. The remaining reads were mapped using Bowtie2 to the mm10 genome.
Duplicate mapped reads were removed using samtools.
The repeat-filtered, duplicate-removed mappings were processed for peak calling by GenRich in groups of 4 replicates each.
The GenRich bedgraphish output files were filtered for peaks with maximum Q-value of 0.1
Assembly: mm10
Supplementary files format and content: peaks.bed.trk.gz: genome browser bed file of GenRich peak calls for one group of replicates

source_name: cortical FACS-sorted cells

extract_protocol:
50,000 cells were used for each ATAC-seq experiment.
The ATAC-seq libraries were prepared by Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030)

treatment_protocol: The pCAG-EGFP plasmids alone or pCAG-ShhN along with pCAG-EGFP plasmids were electroporated into cortical ventricular zone of wild-type embryos at E13.5. E16 cortices from the electroporated brains were dissected, and cells were dissociated using the Worthington Papain Dissociation Kit. Fluorescence activated cell sorting (FACS) was performed to enriched for the GFP+ cells.

value: cortical FACS-sorted cells

value: wildtp

value: Shh-ires-GFP electroporate


title: Mouse15_TCRb_KO_co_housed

value: Fecal pellets

value: TCRb-/-


title: PBMC of CY0001 on 8Sep20

description: Blood sample taken at one timepoint from CS3392

source_name: PBMC

value: PBMC

value: female

value: whole blood


title: S106_wdah_RU-_gut_rep2


title: DOXY-_ARS+_shMETTL3_FUS-P525L_INP_REP1_S11

description:
SK-N-BE stable cell line with doxycycline inducible FUS-P525L,CONTROL (without doxycycline induction), Arsenite treated, sh-METTL3, Input, Replicate1
counts_table.tsv
gene_quantification_table.FPKM_withoutTMM.tsv

value: SK-N-BE

value: Input


title: S106_wdah_RU-_gut_rep1

value: Gut

value: RU-


title: Mouse13_TCRb_KO


title: Mouse14_TCRb_KO


title: e16_shh_yz016


title: PBMC of CS3392 on 6Dec21


title: e16_shh_yz014


title: Mouse12_TCRb_KO_Transferred

value: Transferred


title: S106_wdah_RU-_fb_rep5

source_name: Fat body

value: Fat body


title: S106_wdah_RU-_fb_rep4


title: PBMC of CS3392 on 27Jul20


title: Mouse17_WT

value: WT


title: PBMC of CS3392 on 3Aug20


title: Mouse11_WT


title: e16_shh_yz007


title: e16_shh_yz006


title: Mouse10_WT


title: PBMC of CS3392 on 12Aug20


title: S106_wdah_RU-_fb_rep2


title: S106_wdah_RU-_fb_rep3


title: PBMC of CS3392 on 17Jul20


title: e16_shh_yz005


title: Mouse9_WT


title: e16_shh_yz001


title: PBMC of CM3391 on 6Dec21

description: Blood sample taken at one timepoint from CM3391


title: PBMC of CS3392 on 10Nov20


title: S106_wdah_RU-_fb_rep1


title: Mouse8_TCRb_KO_co_housed


title: e16_shh_yz010


title: Mouse7_TCRb_KO_co_housed


title: Bone Marrow of CS3392

description: Fresh bone marrow sample

source_name: Bone Marrow

value: Bone Marrow

value: fresh tissue


title: S106_wdah_RU+_gut_rep4

value: RU+


title: Mouse6_TCRb_KO


title: Lymph node, Stereo-seq

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
For data processing, the FASTQ files underwent analysis using the STOmics Analysis Workflow (SAW) v4.1.0 with default parameters.
Alignment to the reference genome (hg38) was performed using STAR
Data normalization and unsupervised clustering were conducted on gene matrices of 37.5 μm (bin 50) using Seurat V3.
Cell-type annotation involved assessing both gene expression and enrichment analysis through the utilization of EnrichR.
Visual representation of gene expression was achieved using STEREOMAP (v2.0.2), which illustrated cell distribution in gene matrices of 15 μm (bin 20).
Assembly: hg38
Supplementary files format and content: castleman_stomics_BinSize_50_noFiltering.rds: Serialized R data file that contains the spatially resolved and annotated clusters of the lymph node from an individual affected by Idiopathic Multicentric Castleman Disease
Library strategy: Spatial Transcriptomics

source_name: lymph node

extract_protocol:
The lymph node tissue was embedded with pre-chilled Tissue-Tek optimum cutting temperature (OCT) compound (Sakura, 4583) and snap-frozen in liquid nitrogen until the OCT was completely solid
he tissue was cryosectioned at a thickness of 10 μm and then placed in a pre-chilled Stereo-seq capture chip, and libraries were prepared following the standard manufacturer's protocol as previously described (MiRXES, Singapore).

value: lymph node

tag: disease state


title: e16_ctl_yz012

value: cortical FACS-sorted cells

value: wildtp

value: GFP electroporate


title: S106_wdah_RU+_gut_rep1


title: e16_ctl_yz008


title: S106_wdah_RU+_gut_rep3


title: Mouse5_TCRb_KO_Transferred

value: Fecal pellets

value: TCRb-/-


title: Mouse4_TCRb_KO_Transferred


title: S106_wdah_RU+_gut_rep2


title: TGIRT RNAseq SETX KO rep2

city: Austin

first: Tanya

middle: T.

last: Paull

state: TX

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

description:
SETX_KO_HX46,_47,_48 TGIRT RNAseq CHM13T2T.bigwig
SETX_KO_HX46,_47,_48 TGIRT RNAseq CHM13T2T_positive_strand_reads.bigwig
SETX_KO_HX46,_47,_48 TGIRT RNAseq CHM13T2T_negative_strand_reads.bigwig

data_processing:
R-ChIP: Libraries were sequenced by the UT Genomic Sequencing and Analysis Facility (RRID:SCR_021713) using the Illumina NovaSeq SP platform with PE150 runs. Sequencing reads were cleaned using FASTP in paired end mode and mapped to the genome using BWA-MEM with default values and the CHM13_T2T genome build. Aligned reads were converted to bedgraph format via MACS2 (Zhang et al. 2008). Output bedgraph files were processed again using MACS2’s bdgcmp command with the ppois flag to approximately remove the ChIP input influence from the ChIP bedgraph files. Finally, bedgraph output was read depth normalized to make files equivalent in total signal by converting to bigwig format, quantification with multibigwigsummary, and scaling with bigwigcompare at 1 nt resolution.
TGIRT RNA-seq: Sequencing reads were cleaned using FASTP in paired end mode and mapped to the genome using HISAT2 (Kim et al. 2019) with default values and the CHM13_T2T genome build using the strand specific flag FR. Bam files from biological replicates were merged using samtools merge and converted to bigwig format using bamcoverage (Ramírez et al. 2016). For non-strand-specific processing, bigwig files were read depth normalized to make files equivalent in total signal by quantification with multibigwigsummary followed by scaling with bigwigcompare at 1 nt resolution. For strand-specific processing, merged bam files were converted to sam format using BAM-to-SAM. Awk was used to extract positive strand reads with {if(($1 ~ /^@/) || ($0 ~ /XS:A:\+/)) print $0} or negative strand reads with {if(($1 ~ /^@/) || ($0 ~ /XS:A:-/)) print $0}. Sam files were converted back into bam format using SAM-to-BAM and then converted to bigwig format using bamcoverage (Ramírez et al. 2016). Bigwig files were read depth normalized to make files equivalent in total signal by scaling with bigwigcompare at 1 nt resolution with scaling factors derived from non-strand-specific comparison.
Assembly: CHM13T2T
Supplementary files format and content: R-ChIP: bigwig; TGIRT: bigwig, bulk or strand-specific, as indicated

growth_protocol: DMEM, 10% fetal bovine serum, high glucose, glutamine media, 37 degrees C, 5% CO2

extract_protocol:
R-ChIP: U2OS cells with expression of human RNaseH1 (D210N)-flag (one 150 mm dish per biological replicate) were crosslinked by addition of formaldehyde (1% final concentration) at RT for 7 min, followed by glycine (125 mM final concentration) at RT for 15 min. Cells were washed twice with cold PBS and harvested by scraping. Cells were pelleted at 3,000 rpm for 10 min in 15 ml Falcon tubes. Cell pellets were washed twice with 1 ml cell lysis buffer (10 mM Tris pH8, 10 mM NaCl, 0.5% (vol/vol) Igepal CA-630, and protease inhibitors (Pierce # A32955; 1 tablet per 10 ml)). Then each cell pellet was resuspended in 2.2 ml of RIPA buffer (50 mM Tris pH8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% Sodium Deoxycholate, 1% NP40, and protease inhibitors) and sonicated with a Bioruptor sonicator for 2×15 min at high power 15 sec on and 15 sec off. The extract was cleared with 3,500 rpm centrifugation at 4˚C for 5 min. A 50 μl aliquot of the supernatant was saved as the ‘Input’ sample, 1 ml of supernatant was transferred to 1.5 ml tube containing Pierce Protein A/G Magnetic Beads pre-incubated with anti-flag antibody (5 μg; Sigma, F1804-1MG), another 1 ml of supernatant was transferred to beads-only tube as negative control, and immunoprecipitated overnight with rotation at 4˚C. The next day, the beads were washed 3 times each with wash buffer I (20 mM Tris pH8, 2 mM EDTA, 150 mM NaCl, 1% Triton, 0.1% SDS), wash buffer II (20 mM Tris pH8, 2 mM EDTA, 500 mM NaCl, 1% Triton, 0.1% SDS), and 1 time with wash buffer III (10 mM Tris pH8, 1 mM EDTA, 1% Sodium Deoxycholate, 250 mM LiCl, 1% NP40), each wash was 3 min at RT. Beads were then washed with TE buffer (10 mM Tris pH8, 1 mM EDTA) and transferred to a fresh tube with 100 μl elution buffer (1% SDS, 100 mM NaHCO3).  Samples were eluted by shaking at 30˚C for 30 min. The beads were then pelleted, and the supernatant was transferred into a fresh tube. The tube containing the supernatant was incubated at 65˚C overnight. The DNA samples were purified (Qiagen quick nucleotide removal kit, #28304) and eluted with 50 μl TE buffer.
TGIRT RNA-seq: total RNA was extracted from U2OS lysates using the mirVana miRNA isolation kit (Thermo Fisher) according to manufacturer instructions. 10 μg RNA was incubated with Baseline-ZERO DNase (Lucigen; 2 units, 30 min at 37 ̊C) to digest DNA followed by rRNA depletion using an Illumina RiboZero Gold (Human/Mouse/Rat) kit. The rRNA-depleted RNAs were then cleaned up with a Zymo RNA clean and concentrator kit by using the manufacturer's two-fraction protocol to separate long and short RNAs. The long RNAs (>200 nt) were chemically fragmented to 70-90 nt length by using an NEBNext Magnesium RNA Fragmentation Module (New England Biolabs; 94 ̊C for 5 min) and cleaned up with a Zymo RNA clean and concentrator kit using a modified 8X ethanol protocol (v/v ratio 1:2:8 for RNA sample: kit RNA Binding Buffer: 100% ethanol) to minimize loss of very small RNAs. The chemically fragmented long RNAs were then combined with the non-chemically fragmented short RNAs (<200 nt), and the reconstituted total RNAs were treated with T4 polynucleotide kinase (Lucigen; 50 U for 30 min at 37  ̊C) to remove 3' phosphates and 2',3'-cyclic phosphates, which impede TGIRT template switching, followed by a final clean-up with a Zymo RNA clean and concentrator kit using the modified 8X ethanol protocol above. For all samples, RNA concentration and quality were checked by mRNA assay with a Pico Kit on an Agilent 2100 Bioanalyzer. The recovered RNAs (2-50 ng for cellular RNAs) were used for TGIRT-seq library preparation.
R-ChIP samples (2 biological replicates per condition plus input samples) were used to prepare DNA libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) with NEBNext Multiplex dual index primers using 12 amplification cycles and 2 additional AMPure XP clean-up steps at 0.8X according to manufacturer's instructions.
TGIRT RNA-seq library preparation: TGIRT-seq libraries were constructed as described (Xu et al. 2021, 2019) by using TGIRT-template switching from a synthetic RNA template/DNA primer duplex to the 3' end of the target RNA for 3' RNA-seq adapter addition and a single-stranded DNA ligation to the 3' end of the cDNA using Thermostable 5’ AppDNA/RNA Ligase (New England Biolabs) for 5' RNA-seq adapter addition. The TGIRT-template switching reaction was done with 1 μM TGIRT-III RT (InGex, LLC) for 15 min at 60°C). The resulting cDNAs were amplified by PCR with primers that add capture sites and indices for Illumina sequence (denaturation 98°C for 5 sec, followed by 12 cycles of 98°C for 5 sec, 65°C for 10 sec, and 72°C for 10 sec) The PCR products were purified by using Agencourt AMPure XP beads (Beckman Coulter), and the libraries were sequenced on an Illumina NextSeq 500 to obtain 2 x 75-nt paired-end reads.

value: osteosarcoma

value: SETX knock out


title: e16_ctl_yz004


title: S106_wdah_RU+_fb_rep5


title: TGIRT RNAseq SETX KO rep1


title: Mouse2_WT


title: S106_wdah_RU+_fb_rep4


title: TGIRT RNAseq shSETX rep3

description: shSETX_HX40,_41,_42_TGIRT RNAseq CHM13T2T.bigwig

value: wild-type

value: SETX-depleted (shRNA)


title: Mouse3_WT


title: LargeWhite pig muscle, replicate2, 5-day-old, Input

city: wuhan

first: gu

last: hao

address: 29 Nanhu Avenue, Shizishan Street

institute: Hubei Academy of Agricultural Sciences

data_processing:
Raw sequencing fastq files were assessed for quality, adapter content and duplication rates with FastQC v0.11.9
trimmed using trimmomaticv0.38and aligned with hisat2v2.2.1 to either the piggenome usingsusScr11versions fromdatabasename.
Methylation modification regions were identified by peak calling for each sample separately using exomepeak v2.17.0
the different peak between groups were determined using exomepeak
peaksand different peaks wereannotated to the positionof genesusing ChIPseeker v1.30.2.The motifs were analyzed using homer.
Assembly: susScr11
Supplementary files format and content: tab-delimited txt files include peak counts for each sample.

organism: Sus scrofa

source_name: longissimus dorsi

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific) and the concentration of total RNA were measured by Qubit RNA HS Assay. mRNA was isolated from 75 ug of total RNA using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific). The purified mRNA was then fragmented in 1X RNA Fragmentation Buffer (Thermo Fisher Scientific) at 70℃ for 5 min. After purification, the fragmented RNA was used for enrichment with 5 ug of m6A antibody (Synaptic Systems) which were previously incubated with 25ul of protein A/G magnetic beads mixture (Thermo Fisher Scientific). The incubation was performed at 4℃ for 4h with rotation. After immunoprecipitation, the magnetic beads were washed 3 times using IP buffer (150 mM NaCl, 10 mM Tris-HCl pH 7.5, 0.1% IGEPAL CA-630 in nuclease-free H2O) for 10 min of each time at 4℃ with rotation. Finally, the m6A modified mRNA fragments were extracted by Trizol reagent and purified with RNA Clean & Concentrator™ Kit (Zymo Research)
After purification, both m6A antibody enriched RNA and partial of unenriched mRNA after fragmentation which was used as input was constructed library using VAHTS® mRNA-seq V3 Library Prep Kit for Illumina(Vazyme) according to the manufacturer’s protocol.
MeRIP-seq

value: longissimus dorsi

tag: breed

value: LargeWhite


title: LargeWhite pig muscle, replicate3, 5-day-old, Input


title: S106_wdah_RU+_fb_rep3

value: Fat body


title: Mouse1_WT

value: WT


title: e16_ctl_yz011


title: TGIRT RNAseq shSETX rep2


title: LargeWhite pig muscle, replicate1, 5-day-old, Input


title: S106_wdah_RU+_fb_rep2


title: NingXIANG pig muscle, replicate3, 5-day-old, Input

value: NingXIANG


title: TGIRT RNAseq shSETX rep1


title: hippocampal cultures, shControl, 0h Bicuculline, rep4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCm38.p6
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

source_name: primary hippocampal cultures

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: primary hippocampal cultures

value: UNC

value: minusBic


title: hippocampal cultures, shControl, 0h Bicuculline, rep3


title: S106_wdah_RU+_fb_rep1

value: RU+


title: NingXIANG pig muscle, replicate2, 5-day-old, Input


title: TGIRT RNAseq SETX KO rep3


title: TGIRT RNAseq control rep2

description:
shCntrl_HX37,_38,_39_TGIRT RNAseq_CHM13T2T.bigwig
shCntrl_HX37,_38,_39 TGIRT RNAseq CHM13T2T_positive_strand_reads.bigwig
shCntrl_HX37,_38,_39 TGIRT RNAseq CHM13T2T_negative_strand_reads.bigwig


title: S106_XBP1U_RU-_gut_rep4

value: Gut

value: RU-


title: S106_XBP1U_RU-_gut_rep3


title: hippocampal cultures, shControl, 0h Bicuculline, rep1


title: hippocampal cultures, shControl, 0h Bicuculline, rep2


title: LargeWhite pig muscle, replicate3, 5-day-old, MeRIP-seq


title: TGIRT RNAseq control rep3


title: TGIRT RNAseq control rep1


title: S106_XBP1U_RU-_gut_rep2


title: hippocampal cultures, shControl, 4h Bicuculline, rep4


title: S106_XBP1U_RU-_gut_rep1


title: LargeWhite pig muscle, replicate2, 5-day-old, MeRIP-seq


title: hippocampal cultures, shControl, 4h Bicuculline, rep3


title: SETX KO rep2 input

value: input DNA


title: LargeWhite pig muscle, replicate1, 5-day-old, MeRIP-seq


title: SETX KO rep1 input


title: S106_XBP1U_RU-_fb_rep3


title: NingXIANG pig muscle, replicate3, 5-day-old, MeRIP-seq


title: control rep2 input


title: S106_XBP1U_RU-_fb_rep2


title: hippocampal cultures, shControl, 4h Bicuculline, rep1


title: NingXIANG pig muscle, replicate2, 5-day-old, MeRIP-seq


title: S106_XBP1U_RU-_fb_rep1


title: hippocampal cultures, shDnmt3a1, 0h Bicuculline, rep4


title: NingXIANG pig muscle, replicate1, 5-day-old, Input


title: S106_XBP1U_RU+_gut_rep4


title: NingXIANG pig muscle, replicate1, 5-day-old, MeRIP-seq


title: R-ChIP SETX KO rep2

description: XW7,8 RChIP CHM13T2T.bigwig

value: inactive RNaseH1 ChIP


title: R-ChIP SETX KO rep1

description: XW7,8 RChIP CHM13T2T.bigwig

value: osteosarcoma


title: WT_MouseNo_7

data_processing:
Raw fastq files were first filtered by fastp (v0.22.0) to trim and remove sequencing adapters as well as low quality bases and reads.
Trimmed fastq files were then aligned to mm10 (UCSC) with bowtie2(v2.5.2) under default parameters.Reads that cannot aligned to mouse genome were extracted by samtools (v1.18)
Clean fastq files were analyzed by Kraken2 (v2.0.7-beta) software using Standard PlusPF (release 1/12/2024) database downloaded from index zone (https://benlangmead.github.io/aws-indexes/k2).
Assembly: mm10
Assembly: Kraken 2 / Bracken Refseq index
Supplementary files format and content: Table separated files containing taxonomy counts of each sample.
Supplementary files format and content: Table separated files containing KEGG orthology gene counts of each sample.
Library strategy: metagenome sequencing

source_name: Fecal

growth_protocol: TCRb-/- mice were freshly ordered from the Jackson laboratory

extract_protocol:
Feces were collected and DNA was extracted by QIAGEN Power Fecal Pro DNA Kit following manufacturer's instruction.
mWGS DNA library was constructed using TruSeq DNA Library Prep Kit under manufacturer's instruction for metagenomic whole-genome shotgun sequencing (mWGS)

tag: host

value: mouse

tag: host tissue

value: feces


title: WT_MouseNo_6


title: R-ChIP control rep2

description: XW5,6 RCHIP CHM13T2T.bigwig

value: wild-type

tag: antibody


title: S106_XBP1U_RU+_gut_rep3


title: hippocampal cultures, shDnmt3a1, 0h Bicuculline, rep3


title: S106_XBP1U_RU+_gut_rep2


title: S106_XBP1U_RU+_gut_rep1


title: WT_MouseNo_4


title: WT_MouseNo_5


title: hippocampal cultures, shDnmt3a1, 0h Bicuculline, rep1


title: PBS Single Nuclei Mulitome RNA-seq

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 Euclid

institute: Washington University in St. Louis

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Supplementary files format and content: Processed files for scRNA-seq are barcodes.tsv, features.tsv, matrix.mtx ; for snATAC-seq atac_fragment.tsv, atac_peaks.bed, matrix.h5, and per_barcode_metrics.csv

source_name: Islet of Langerhands

extract_protocol:
Library construction for single cell was constructed using 10X Chromium Protocol.
single cell multiplexed gene expression, Single Nuclei Mulitome Gene Expression and ATAC sequencing

treatment_protocol: scRNA-seq islets were treated for 48-hr with 1,000 ng/mL IFNγ + 500 ng/mL TNFα+100 ng/mL IL1β ;  1,000 ng/mL IFNγ+100 ng/mL IL1β; 100 ng/mL IL1β ; 1,000 ng/mL IFNγ; 500 ng/mL TNFα ; 10 μM.     For multiomic sequencing we treated human islets  (1) 24 hrs DMSO, (2) 48 hrs PBS+0.1%BSA, (3) 24 hr 0.1 ug/mL Brefeldin A, (4) 48 hr Cytokine mix (1,000 ng/mL IFNγ, 500 ng/mL TNFα, 100 ng/mL IL1β. thapsigargin (TG), or 1 ug/mL brefeldin A (BFA) or DMSO

value: Islet of Langerhands

value: Primary

tag: kit used

value: 10x Single Cell Multiome ATAC + Gene Expression v1 kit

value: PBS


title: S106_XBP1U_RU+_fb_rep4

value: Fat body


title: hippocampal cultures, shControl, 4h Bicuculline, rep2

value: primary hippocampal cultures


title: hippocampal cultures, shDnmt3a1, 4h Bicuculline, rep3


title: control rep1 input


title: WT_MouseNo_3

value: WT


title: PBS Single Nuclei Mulitome ATAC-seq


title: S106_XBP1U_RU+_fb_rep3


title: S106_XBP1U_RU+_fb_rep2


title: hippocampal cultures, shDnmt3a1, 4h Bicuculline, rep2


title: WT_MouseNo_1


title: hippocampal cultures, shDnmt3a1, 4h Bicuculline, rep1


title: WT_MouseNo_2


title: CM Single Nuclei Mulitome RNA-seq


title: hippocampal cultures, shDnmt3a1, 0h Bicuculline, rep2

value: minusBic


title: CM Single Nuclei Mulitome ATAC-seq


title: R-ChIP control rep1

description: XW5,6 RCHIP CHM13T2T.bigwig


title: DMSO Single Nuclei Mulitome RNA-seq

value: DMSO


title: S106_XBP1U_RU+_fb_rep1

value: RU+


title: Tcrb_KO_MouseNo6

value: Tcrb-/-


title: hippocampal cultures, shDnmt3a1, 4h Bicuculline, rep4


title: S106_XBP1S_RU-_gut_rep3

value: Gut

value: RU-


title: Tcrb_KO_MouseNo7


title: S106_XBP1S_RU-_gut_rep2


title: BFA Single Nuclei Mulitome RNA-seq

value: Brefeldin A


title: S106_XBP1S_RU-_gut_rep1


title: Tcrb_KO_MouseNo4

value: mouse


title: DMSO Single Nuclei Mulitome ATAC-seq


title: BFA Single Nuclei Mulitome ATAC-seq


title: Tcrb_KO_MouseNo3

value: feces


title: Patient 3

value: 10X single cell 3'

value: BFA, Thapsigargin, DMSO, Cytokines


title: S106_XBP1S_RU-_fb_rep4


title: Tcrb_KO_MouseNo2


title: S106_XBP1S_RU-_fb_rep3


title: S106_XBP1S_RU-_fb_rep2


title: Patient 2

value: Islet of Langerhands

value: Primary


title: Patient 1


title: 72hr Male Negative

city: Towada

first: Asako

last: Haraguchi

state: Aomori

department: School of Veterinary Medicine

country: Japan

institute: Kitasato University

data_processing:
FastQC v0.11.7 was used for performing quality check on the raw sequences before analysis to make sure data integrity.
Trimmomatic 0.38 was used for trimming to remove low quality reads, adaptor sequence, contaminant DNA, or PCR duolicates.
Trimmed reads were mapped to reference genome with HISAT2. Transcript was assembled by StringTie with aligned reads.
Expression profiles were represented as read count and FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value as a normalized value.
Assembly: AsteI2
Supplementary files format and content: The data file is text file and includes expressioin profiles of each samples.

organism: Anopheles stephensi

source_name: Whole body

extract_protocol:
Three mosquitoes were collected as one sample and stored at -80 °C. Total RNA was extracted using Nucleo Spin RNA Blood (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol, delivered to Macrogen Japan Corp. (Tokyo, Japan) for library construction using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).
Total RNA was sequenced using the NovaSeq 6000 system (Illumina).

value: Whole body

tag: gender

value: Male

value: Medium injection

tag: timepoint


title: S106_XBP1S_RU-_fb_rep1

value: Fat body